Steps to reproduce:

1. Open the attached project
2. Open and play the 'CompoundTriggerCorruption' scene
3. Notice that as the sphere enters a cube, the color of the cube is changed and the OnTriggerEnter and OnTriggerExit is logged in the console
4. In the third iteration (when only the cube on the left is activated) notice that the OnTriggerExit is called too early

Workaround: Deactivate and activate the parent object with the rigidbody (RigidbodyBase game object) before setting the state of the child objects.